SOX9 and endometriosis: Peritoneal lesions upregulated markers of PE (SOX9+ and pre‐ciliated) versus peritoneum and Upregulated markers for SOX9+LGR5+ subset (WNT7A, KRT17) as in PE. In contrast, secretory cell PAEP and SCGB2A2 and ciliated cell PIFO, TP73 epithelial markers, are ~ to peritoneum. Conclusion: Dysfunctional epithelium is a major driver of endometrial disease with two SOX9 populations dominant in endometriosis.